[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

[Anurag Dobhal]

How to iteration the system 26 times. I am unable to understand that part.

please explain how to do it.

Thank you

On Fri, Oct 3, 2014 at 3:51 PM, Anurag Dobhal <
anurag.dobhal at nano-medicine.co.in> wrote:

> hello Justin thanks for your reply.
>
> I am unable to understand how to proceed in this tutorial. I am working on
> it from many days but I am unable to do.
>
> I have understood till the step.
>
> perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
>
> this is the result which I got.
>
> Area per protein: 2 nm^2
> Area per lipid: 10.4716089904762 nm^2
>
> Area per protein, upper half: 1.75 nm^2
> Area per lipid, upper leaflet : 10.4755772444444 nm^2
>
> Area per protein, lower half: 2 nm^2
> Area per lipid, lower leaflet : 10.4716089904762 nm^2
>
> Writing Area per lipid...
> Done!
>
>
> and the minimization step after that. I get the confout.gro file.
>
>
> I am confused how to continue from the step
>
> "perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat"
>
> how many times do we need to run this command, nd with what changes ????
>
> and how to solvate the system  ( which file ) and what will be the command ???
>
> looking for your kind reply.
>
> please help.
>
> Thank you
>
>
>
> On Thu, Oct 2, 2014 at 10:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/2/14 12:51 PM, Anurag Dobhal wrote:
>>
>>> how will I get to know that the system have shrunken enough, and which
>>> file
>>> I need to solvate.
>>>
>>>
>> This is stated in the tutorial.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
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>
>

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